Showing : scrnaseq • reset
5
votes
13
replies
996
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 17 days ago by 53k • written 29 days ago by • 0
0
votes
1
reply
145
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
6 weeks ago • updated 5 weeks ago Francesco Silvestro • 0
1
vote
10
replies
1.1k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 16 days ago by • 0 • written 7 weeks ago by • 0
1
vote
2
replies
263
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 8 weeks ago by 53k • written 8 weeks ago by • 0
0
votes
11
replies
819
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
9 weeks ago • updated 8 weeks ago Peter Hickey ▴ 760
0
votes
3
replies
883
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 7 months ago by 43k • written 7 months ago by • 0
0
votes
0
replies
308
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
7 months ago Muhammad • 0
0
votes
3
replies
802
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 months ago by • 0 • written 8 months ago by ▴ 10
2
votes
2
replies
785
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 13 months ago by ▴ 10
0
votes
0
replies
704
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
15 months ago Damini • 0
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 15 months ago by 53k • written 15 months ago by • 0
0
votes
0
replies
604
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
16 months ago Bibi • 0
0
votes
1
reply
917
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
2
replies
991
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
19 months ago rocanja ▴ 60
0
votes
1
reply
710
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
1
vote
2
replies
1.9k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
22 months ago ruba-mahmoud • 0
0
votes
2
replies
1.3k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.0 years ago Momo • 0
0
votes
1
reply
812
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
votes
5
replies
1.7k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.2 years ago duez.tolga • 0
0
votes
1
reply
2.7k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
4
votes
3
replies
1.6k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
0
votes
1
reply
880
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
1
reply
938
views
library(topGO) query
topGO scRNAseq
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
0
votes
0
replies
740
views
adding noise to scRNA Seq counts
scRNAseq
2.2 years ago Jiyuan • 0
1
vote
11
replies
9.3k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 23 months ago by • 0 • written 2.3 years ago by • 0
2
votes
3
replies
2.1k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.3 years ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
979
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.4 years ago info ▴ 10
0
votes
1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.5 years ago by 4.2k • written 2.5 years ago by ★ 1.6k
2
votes
0
replies
2.5k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.5 years ago Tadeoye ▴ 20
0
votes
1
reply
1.5k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ▴ 10
4
votes
5
replies
2.8k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 23 months ago by • 0 • written 2.6 years ago by • 0
0
votes
3
replies
2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 15 months ago by • 0 • written 2.9 years ago by • 0
1
vote
2
replies
2.0k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
3.0 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.5k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.0 years ago evocanres • 0
0
votes
3
replies
1.7k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.0 years ago Madiha • 0
4
votes
5
replies
4.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.2 years ago Peter Hickey ▴ 760
4
votes
2
replies
1.8k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.2 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 40
0
votes
0
replies
1.4k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.2 years ago peter.kharchenko ▴ 30
0
votes
0
replies
1.1k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.2 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.9k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.2 years ago Chise ▴ 10
0
votes
0
replies
1.6k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.3 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.7k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
1
reply
1.7k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
votes
8
replies
2.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.3 years ago Kelen ▴ 10
0
votes
1
reply
1.1k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
1
vote
2
replies
3.0k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.5 years ago Ismail • 0
1
vote
1
reply
2.8k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.5 years ago by ▴ 760 • written 3.5 years ago by • 0
2
votes
2
replies
2.1k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.6 years ago behr201 • 0
95 results • Page 1 of 2
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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